Whole Genome Sequencing aka “WGS” - utility in foodborne illness outbreak detection and investigations Dan Rice FDA ORA – Pacific Regional Lab Northwest
Jan 03, 2016
Whole Genome Sequencingaka “WGS” - utility in
foodborne illness outbreak detection and investigations
Dan RiceFDA ORA – Pacific Regional Lab Northwest
Foodborne illness in the US We have one of the safest food supplies in world but burden of
illness still high
Estimated 1 in 6 Americans (48 million people) sick annually with foodborne illness 128,000 hospitalizations 3,000 deaths
Annual laboratory confirmed cases in US Campylobacter – 43,696 Salmonella – 41,930 E. coli O157 – 3,704 Shiga-toxin producing E. coli (STECs) – 1,579 Listeria monocytogenes – 808
JAMA June 18, 2014 311(23): 2374
We still have work to do….
http://www.cspinet.org/new/200910061.html
http://www.nextgenerationfood.com/news/risky-food-list/
The 10 Riskiest Foods
PulseNet Network of public health labs Perform standardized
protocols of PFGE on: Salmonella enterica Campylobacter ssp. E. coli O157 and other
Shiga-toxin producing E. coli (STECs)
Listeria monocytogenes Shigella spp.
Data sharing in private network
PFGE Patterns of L.
monocytogenes isolates
associated w/alfalfa sprouts
L. monocytogenes - Outbreaks and Incidence, 1978-1997
Before PulseNet (20 years)1978-19975 outbreaksMedian 69 cases/outbreak
1989: hot dogs detected as source1985: large cheese
outbreak
No. outbreaksIncidence (per million pop)
SOURCE: John Besser (CDC)
L. monocytogenes - Outbreaks and Incidence, 1978-2003
Before PulseNet (20 years)1978-19975 outbreaksMedian 69 cases/outbreak
PulseNet’s first years(6 years)1998-200314 outbreaksMedian 11 cases/outbreak
1998: PulseNetbegan
1989: hot dogs detected as source1985: large cheese
outbreak
No. outbreaksIncidence (per million pop)
SOURCE: John Besser (CDC)
L. monocytogenes - Outbreaks and Incidence, 1978-2012
Before PulseNet (20 years)1978-19975 outbreaksMedian 69 cases/outbreak
PulseNet’s first years(6 years)1998-200314 outbreaksMedian 11 cases/outbreak
Listeria Initiative & PulseNet (9 years)2004-201228 outbreaksMedian 5.5 cases/outbreak
No. outbreaksIncidence (per million pop)
SOURCE: John Besser (CDC)
Changes in technology (1983-2014)1983 First Cell Phone: Weighed 2.5lbs and could only be used for 20min before the battery died.
Use: phone calls; not widely adopted until late 1990’s/early 2000’s
Apple iPhone 6: Up to 24hr of phone talk time; up to 16 days of standby time; weighs 4.55 oz; 128GB on board storage;
Use: Phone calls, texts, web browsing, fitness tracking, photo/videos, GPS tracking, books, music, movies, games, and the list keeps growing….
Why replace PFGE with WGS?
PFGE served practical public health function but data are qualitative
Whole genome sequencing (WGS) reveals complete DNA make-up of organism, better resolution both within and between species.
Public health labs now using WGS to perform foodborne pathogen identification during foodborne illness outbreaks
Why replace PFGE with WGS?
Whole genome sequencing performs same function as PFGE but also differentiates strains of foodborne pathogens, no matter what the species
Used to determine important information such as;SerotypeVirulence attributesAntibiotic resistanceOther novel markers
Technology works on all microorganisms, ideal for laboratories that support public health
Why develop a WGS based network? Tracking and Tracing of food pathogens
Faster identification of the food involved in the outbreakGlobal travelGlobal food supply IT infrastructure exists
WGS is high resolution 3-5 million data points are collected for each isolate vs. 12 – 24
agarose gel bands
WGS analyses statistically robust Unlike PFGE patterns, WGS data analyzed in evolutionary
context. Accurate and stable genetic changes within pathogen genomes enable ID of specific common sources of outbreak strains (farms, processing plants, food types, and geographic regions).
Source Tracking is Key Application
PFGE v/s WGS
Same PFGEbut not part of the outbreak
Outbreak Isolates2-5 SNPs
SNP phylogeny for S. Bareilly strains
Is WGS a viable solution?• Cost • Increasing ease of
operation• Database longevity• Comparable times to
conventional pipelines• Sample prep
– Identical for all pathogens
• Cost savings– Resistance, subtyping,
virulence factors, more…
• New applications– tracking,
regulatory/compliance actions, historical trends, more…
2007 2008 2009 2010 2011 2012 2013$0
$500
$1,000
$1,500
$2,000
$2,500
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$3,500
Cost per bacterial genome
Illumina Miseq
454
$70/genome in 2014
$40/genome in 2015 w/
Illumina NextSeq Technology
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Timeline for traditional approach to foodborne illness investigation using PFGE
Contaminated foodenters commerce
Identify contaminated food and confirm that product or
environmental samplePFGE pattern match clinical
sample pattern
Identify illnesses and get PFGE pattern from
clinical samples
Source of contaminationidentified too late to prevent most illnesses
CDC FDA/FSIS
Nu
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Timeline for foodborne illness investigationusing WGS
Contaminated food enterscommerce
Local, state and federal agencies use WGS in real-time and in parallel on clinical, food,
and environmental samples
Source of contaminationidentified early through WGS combined database queries
Averted Illnesses
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From C. Darwin's, “On the Origin of Species” - 1859
“It is obvious that the Galapagos Islands would be likely to receive colonists, whether by occasional means of transport or by formerly continuous land, from America; and the Cape de Verde Islands from Africa; and that such colonists would be liable to modification;— the principle of inheritance still betraying their original birthplace"
With WGS, we now have the ability to discern those birthplaces…
I
Detection
(species)
II
Identification
(serotype)
III
Traceback
(subtype)
Is a pathogenthere?
What kind ofpathogen is it?
Is it part of the outbreak?
Next-Generation Sequencing
qPCR/amp-based tech
Maldi-TOF MS/X-MAP
Investigating Food Contamination Events with OMICS ApproachesGetting to the information needed faster and with more precision
Health and economic impact of active WGS-based surveillance
Comparison of 2 related Salmonella contamination events
Similar facilities – broad domestic distribution
Nut butter 1 WGS not used: 42 cases and 10 hospitalizations with estimated 1,260 unreported illnesses (Fall 2012)
Nut butter 2 WGS used: – 4 confirmed cases, 1 hospitalization (Summer 2014)
WGS informed investigation prevented significant illness and hospitalizations
Current status WGS network reliable – efficient, provides very good location specificity of
outbreaks
FDA GenomeTrkr program sequenced >15,000 Salmonella and > 4,000 Listeria monocytogenes. Current rate about 1 genome per hour.
Need for increased number of well-characterized environmental (food, water, facility, etc.) sequences may outweigh need for extensive clinical isolates
Highly successful partnership between FDA, CDC and local/state public health labs on real-time tracking of FB illness outbreaks
Lessons learned WGS works – demonstrates value whenever used.
Use in tracebacks and to limit scope of food contamination events is unprecedented – numerous offshoot food safety applications exist (i.e., compliance, quality assurance, risk assessment)
Development of international open source databases promote WGS-based sentinel surveillance on a global scale
WGS more than just an “Epi-tool” - provides information on AMR, virulence, serotype, and other critical factors in one assay, including historical reference to pathogen emergence
WGS international/global ramifications to policy making (trade, commerce)
WGS for the national interest
Well established in foodborne illness systems – could extend into other
areas of infectious disease (Ebola, MERS, Chikungunya, TB, etc.)
Provides sentinel surveillance on a national/global scale for
antimicrobial resistance with real-time capacity for AMR monitoring
Ability to examine historical context and root cause analysis – ID novel
biomarkers and historical acquisition of those markers.
Potential to dramatically reduce health care costs in the US – help find
“patient zero” swiftly and accurately.
Barriers to Moving Forward Culture independent diagnostic assays – reducing
clinical isolates going into PHLs – still need an isolate
to perform WGS
Capacity building (funding and training)
Issues surrounding data and metadata release into
the public domain
Data handling – terabytes or more/isolate
What’s next?
Metagenomics………..
Questions?
Acknowledgements:- Dr. Eric Brown, FDA CFSAN- Dr. Brian Sauders, NY State Food Laboratory
Who kindly shared much of the material for this presentation
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